Theoretical studies on conformational preferences of modified nucleic acid base N6-(N-glycylcarbonyl) adenine

Conformational preferences of modified nucleic acid base N⁶-(N-glycylcarbonyl) adenine, gc⁶Ade, have been investigated using the quantum chemical PCILO (Perturbative configuration interaction using localized orbitals) method. The multidimensional conformational space has been searched using selected grid points formed by combining various torsion angles that take favored values derived from energy variation with respect to each torsion angle individually. The theoretically predicted most stable, minimum energy conformation of the molecule is such that the substituent on N(6) spreads away from the imidazole moiety of the adenine ring, thus keeping distal orientation. The preferred molecular orientation is stabilized by an intramolecular hydrogen bond from N(11)H of the amino acid to N(1) of the adenine. The carboxylic group of the substituent is trurned away in relation to N(11)H…?N(1) and is perpendicular to the plane through the rest of the molecule The alternative stable conformation corresponding to an 0.8 kcal/mol higher energy has a coplanar carboxylic group turned towards the same side as N(11)H…?N(1) and is exhibited in the crystal structure of the nucleoside derivative, gc⁶A. Energetically, the carboxyl group may change its orientation over a wide range, without much destabilization. This suggests probing by the carboxyl group of the molecular environment in the vicinity of the anticodon in tRNA.     

Influence of N(1) protonation on the orientation of the N(6) substituent in hypermodified nucleic acid base N6-(N-glycylcarbonyl) adenine

The influence of protonation at N(1) on the conformational preferences of the N(6) substituent in the modified nucleic acid base N⁶-(N-glycylcarbonyl) adenine, gc⁶Ade, was investigated by the quantum chemical perturbative configuration interaction using localized orbitals (PCILO) method. The preferred orientation of the glycylcarbonyl substituent changes on the protonation of N(1). In the preferred conformation, the carbonyl oxygen O(10) is placed on the same side as N(1)H and provides stabilization through intramolecular hydrogen bonding of O(10) with HN(1). The amino acid component is so oriented that the carboxyl oxygen O(13b) is aligned closely with the N(6)H direction. Thus, the preferred molecular orientation is further stabilized by intramolecular hydrogen bonding involving HN(6) with O(13b). The alternative conformation has 0.5 kcal/mol higher energy than has the preferred conformation. The preferred conformation is about 1 kcal/mol more stable than is the conformation obtained by the flipping of torsion angle β alone, from the favored orientation for the unprotonated gc⁶Ade. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 551–556, 1997     

Conformational preferences of modified nucleic acid bases N6-(Δ2-isopentenyl) adenine and 2-methylthio-N6-(Δ2-isopentenyl) adenine by the quantum chemical PCILO calculations

Conformational preferences of the hypermodified nucleic acid bases N⁶-(Δ²-isopentenyl) adenine, (i⁶Ade) and its 2-methylthio derivative (ms²i⁶Ade) have been investigated theoretically by the quantum chemical perturbative configuration interaction using localized orbitals (PCILO ) method. The predicted most stable conformation of i⁶Ade and ms²i⁶Ade are such that the isopentenyl substituent is oriented away from the imidazole moiety of the adenine ring. The atoms N(6), C(10), and C(11) remain coplanar with the adenine ring for both molecules. However, in contrast to the predicted cis orientation of the C(10)? C(11) bond with respect to the C(6)? N(6) bond in i⁶Ade, the trans orientation is favored for ms²i⁶Ade. The plane of the isopentenyl group is rotated by 120° from that of the purine base in i⁶Ade, whereas rotation by 60° is favored in ms²i⁶Ade. The favored orientation of the methylthio group with respect to the C(2)? N(3) bond is trans; however, the alternative cis arrangement is also quite probable. The conformational implications of the methylthiolation of the isopentenyladenine are brought out in the context of the considerably large range of accessible (β,γ) and χ orientations. The compatible roles of i⁶Ade and ms²i⁶Ade in tRNA are thus understood, besides their distinguishing features.     

Protonation studies of modified adenine and adenine nucleotides by theoretical calculations and (15)N NMR

The acid/base character of nucleobases affects phenomena such as self-association, interaction with metal ions, molecular recognition by proteins, and nucleic acid base-pairing. Therefore, the investigation of proton-transfer equilibria of natural and synthetic nucleos(t)ides is of great importance to obtain a deeper understanding of these phenomena. For this purpose, a set of ATP prototypes was investigated using (15)N NMR spectroscopy, and the corresponding adenine bases were investigated by theoretical calculations. (15)N NMR measurements provided not only acidity constants but also information on the protonation site(s) on the adenine ring and regarding the ratio of the singly protonated species in equilibrium. Substituents of different nature and position on the adenine ring did not change the preferred protonation site, which remained N1. However, for 2-thioether-ATP derivatives a mixed population of N1 and N7 singly protonated species was observed. Reduction of basicity of 0.4-1 pK(a) units relative to ATP was also observed for all evaluated ATP derivatives, except for 2-Cl-ATP, for which K(a) was ca. 10,000-fold lower. To explain the substitution-dependent variations in the experimental pK(a) values of the ATP analogues, gas-phase proton affinities (PA), Delta Delta G(hyd), and pK(a) values of the corresponding adenine bases were calculated using quantum mechanical methods. The computed PA and Delta Delta G(hyd) values successfully explained the experimental pK(a) values. A computational procedure for the prediction of accurate pK(a) values was developed using density functional theory and polarizable continuum model calculations. In this procedure, we developed a set of parameters for the polarizable continuum model that was fitted to reproduce experimental pK(a) values of nitrogen heterocycles. This method is proposed for the prediction of pK(a) values and protonation site(s) of purine analogues that have not been synthesized or analyzed.     

核酸中碱基的氢键作用机理及电子特征理论研究

采用耦合簇量子化学方法 CCSD/aug-cc-pVDZ研究了嘧啶与嘌呤之间的相互作用,利用基函数叠加误差法(BSSE)消除相互作用能误差,并进行了几何结构优化;采用Gaussian 03程序包中的NBO程序分析了二阶稳定化能及自然键轨道.与此同时,应用约化密度函数(RDG)填色等值面图对体系进行了图形化分析,分析了氢键相互作用所在的空间位置和相对强度,以及氢键相互作用的性质,以进一步了解二者的相互作用.结果表明,嘧啶-嘌呤体系的相互作用属于闭合壳层静电相互作用.电子密度跃迁矩阵分析结果表明,激发区域主要集中在N原子和O原子处,涉及的空间广度很大,第一激发态主要涉及前线分子轨道,属于σ→π*或n→π*类型跃迁.     

Spectroscopic studies of poly(N-acyldehydroalanines) containing asymmetric nucleic acid base derivatives as pendant groups

Water-soluble polynucleotide analogs having a poly(N-acyldehydroalanine) {poly(α[–(N-acylamino)acrylate])} backbone were studied by 360-HMz ¹H-NMR, UV, and CD spectroscopies. Significant UV hypochromicity values for the polymers versus monomer model compounds as well as peak shifts in the NMR spectra implied a high degree of base stacking in these systems. The CD spectrum of poly{(-)-2-[2-(thymin-l-yl) propanoamido] propenoic acid} (p(-)TDHA), having an optically active side chain, was remarkably insensitive to the degree of neutralization of the polymer, but was very sensitive to the ionic strength of the solution. Continuous variation mixing experiments revealed no base-pairing interactions between complementary charged polymers, and weak interactions between charged and uncharged polymers and model compounds. These results suggest that the polymers are conformationally restricted in solution.     

叠氮化合物C6H6-n(N3)n(n=1~6)的密度泛函理论研究

运用密度泛函理论, 在B3LYP/6-31G*水平上, 对叠氮化合物C6H6-n(N3)n(n=1~6)进行理论计算, 并对所得到的几何结构进行了振动频率分析. 计算结果表明, 这些化合物是热力学稳定的. 基于自然键轨道理论, 分析了稳定结构的电荷分布及成键情况. 在不破坏苯环和叠氮基的原则下, 设计等键反应计算了这些化合物的生成热, 结果表明, 标题化合物的生成热都很高, 且随着叠氮基数目的增加而线性增大.     

Chiral peptide nucleic acid monomers (PNAM) with modified backbones

Convenient high yielding syntheses of optically pure PNAMs comprising l- or d-serine, l-lysine and l-arginine units linked to thymine or Cbz-cytosine are described. Simple workup and inexpensive reagents are employed and free amino acids are used as coupling components.     

Conformational studies of copoly (N 5-ω-hydroxyalkyl-L-glutamine-L-glutamic acid)s

Copoly (α-amino acid)s consisting ofL-glutamic acid residue andN ⁵-ω hydroxyalkyl-L-glutamine residue, i.e., 2-hydroxyethyl, 3-hydroxypropyl, and di-2-hydroxyethyl derivatives were prepared by the reactions of copoly (L-glutamic acid) containing succinimide ester with corresponding amino alcohols. The conformation of these copolymers was examined by the CD and infrared measurements. These three copolymers containing about 20–30% hydroxyalkyl groups undergo a methanol-induced and a pH-induced conformational transitions. The copolymer containing about 50% 3-hydroxypropyl group assumes the α-helical conformation in the pH region from 2.5 to 11.6, and in a methanol-water mixture (9∶1). On the other hand, the copolymer containing about 60% di-2-hydroxyethyl groups does not allow any helical conformation even at lower pH and also even in a trifluoroethanol-water mixture (9∶1), suggesting that the branched hydroxyalkyl group is unfavorable for the formation of α-helix. Furthermore, the poly(N ⁵-di-2-hydroxyethyl-L-glutamine) is shown to have a rather disordered structure in the solid state.     

TinC2n(n=1-6)分子簇的量子化学从头算研究

用量子化学从头计算方法研究了TinC2n(n=1-6)分子簇的几何构型和电子结构。这些TinC2n分子簇以TiC2为结构单元, 通过C-C或Ti-C键进一步连接而逐渐长大。研究结果可以较好地解释实验现象, 并说明Metcars的形成机理。     

Synthesis and conformational studies of dipeptides constrained by disubstituted 3-(aminoethoxy)propionic acid linkers

A series of cyclic compounds with dimethyl-substituted 3-(aminoethoxy)propionic acid linkers have been prepared as potential beta-turn mimics. The desired linkers were prepared from disubstituted pyrones, which were coupled with dipeptides and then subjected to macrocyclization using diethylcyanophosphonate to furnish cyclic compounds 1-5. Conformational analysis was carried out using NMR and X-ray crystallography. All of the five cyclic compounds were found to exist in type I or type II beta-turn conformations.     

自由基C59N及双体(C59N)2的理论研究

用INDO系列方法对自由基C59N及双体(C59N)2进行了理论研究,结果表明: N的掺入使C60笼发生畸变, N向笼外突出, 碳氮6-6键上的C自旋密度较大, 两C59N自由基在这个碳上以C-C单键连接形成双体为C2h, C2v对称性。其中C2v构型更稳定, 且N与附近的三个碳均以单键连接。理论计算的电子光谱与实验吻合较好。(C59N)2易分解为单体C59N。     

Synthesis of novel analogs of aromatic peptide nucleic acids (APNAs) with modified conformational and electrostatic properties

Aromatic peptide nucleic acid analogs having an N-(2-aminobenzyl)glycine backbone (APNA 1) were previously identified as promising new leads for the design of polyaromatic DNA mimics. Structural modifications of 1, which lock the aromatic backbone into a unique conformation, while maintaining the same space distribution between the nucleobases as in 1, were investigated. The electrostatic potential of the aromatic backbone was also modified in an attempt to improve the solubility of these compounds in aqueous media and to evaluate how the quadrapole of the aromatic backbone may influence the biophysical properties of the APNA oligomers. PNA hexamers containing a single monomer insert of each new APNA monomer were used to explore the hybridization properties of these analogs with poly rA and poly dA. Preliminary results indicated that these modifications do not seriously alter the molecular recognition properties of APNAs towards DNA and RNA.     

15N nuclear magnetic resonance studies of [1-15N]nicotinamide adenine dinucleotides

The synthesis of [1-¹⁵N]nicotinamide adenine dinucleotide is described. Chemical shift data from ¹⁵N NMR studies are presented for the pyridine ring nitrogen of labeled NAD and related compounds. The results indicate a ¹⁵N label in the N-1 position to be highly sensitive to the redox-state of the pyridine moiety, with an upfield shift of over 100 ppm observed upon reduction of NAD⁺ to NADH. The feasibility of conducting ¹⁵N NMR studies of pyridine nucleotide binding to dehydrogenases is discussed.     

Copolymers containing alternating sequences of nucleic acid base pairs. II. Polymerization studies

The objective of this project was to utilize the alternating copolymerizability of electrondonor monomers with electron-acceptor monomers to selectively introduce nucleic acid bases into copolymers in a controlled sequence distribution. To this end, maleimide monomers containing the adenine, thymine, cytosine, and 6-chloropurine moieties were converted to their hompolymers. The homopolymer of 1-(vinyloxyethoxy)thymine was also prepared. Alternating copolymers of the adenine maleimide monomer and the corresponding 6-chloropurine maleimide monomer with 1-(vinyloxyethoxy)thymine were prepared. The latter copolymer was converted to the alternating adenine–thymine copolymer by reaction with ammonia. Characterization of the polymers and copolymers via spectroscopic methods and physical measurements confirm their proposed structures. Monomer syntheses and characterization, as well as studies designed to establish the extent and nature of adenine–thymine interactions in the copolymers, are reported in accompanying papers.     

Copolymers containing alternating sequences of nucleic acid base pairs. III. Spectroscopic studies

A study was conducted of the complementary base pair interactions between various pairs of electron-donor monomers, electron-acceptor monomers, homopolymers and alternating copolymers selected from the following group: ( 1 ) 9-(2-vinyloxyethyl)adenine; ( 2 ) 1-(2-vinyloxyethyl)thymine; ( 3 ) 1-(2-vinyloxyethyl)cytosine; ( 4 ) 9-(2-maleimidoethyl)adenine; ( 5 ) 6-chloro-9-(2-maleimidoethyl)purine; ( 6 ) 1-(2-maleimidoethyl)thymine; ( 7 ) 1-(2-maleimidoethyl)cytosine; ( 8 ) homopolymer of ( 4 ); ( 9 ) homopolymer of ( 6 ); ( 10 ) alternating copolymer of ( 2 ) and maleic anhydride; ( 11 ) alternating copolymer of ( 2 ) and ( 5 ); and ( 12 ) alternating copolymer of ( 2 ) and ( 4 ). By ¹H-NMR, in CDCL₃, the base pair interactions between ( 1 ) and ( 2 ) were shown to be hydrogen bonding, the extent of which was shown by a calculated binding constant, K = 61.81 L/mol. The nature of this interaction was conformed by IR. Neither monomer pairs ( 1 )/( 2 ) nor ( 4 )/( 6 ) exhibited hydrogen bonding in DMSO-d₆. However, hydrogen bonding interaction was observed for DMSO-d₆ solutions of homopolymers ( 8 ) and ( 9 ) and for alternating copolymer ( 12 ). On the basis of an upfield chemical shift of the 2- and 8-aromatic protons of ademine of ( 1 ) in D₂O, a partial overlap stacking interaction is proposed. No charge-transfer interactions could be observed by UV between donor-acceptor monomer pairs.     

Synthesis of poly(vinylamine) containing asymmetric nucleic acid base derivatives as grafted pendants

The preparations of new model polymers of polynucleotides with stereoregular poly(vinylamine) (PVAm) backbones and an optically active nucleic acid base derivative as a pending side chain are described. The grafting of (±)-, (+)-, and (?)-2-(thymin-1-yl) propionic acid to linear PVAm prepared either by hydrolysis of poly(vinyl acetamide) or poly(vinyl-t-butyl carbamate) has proven to be more difficult than the case of polyethyleneimine. This may be due to a combination of the low solubility and steric factors of PVAm. PVAm formed a complex with oximes such as ethyl-2-hydroxyimino cyanoacetate (EHICA), which activates the amino group of PVAm; it became soluble in polar solvents and gave higher percent graft. These carboxylic acid derivatives were grafted onto PVAm through amide bonds by direct coupling with sulfonic acid esters of hydroxybenzotriazoles to give optically active graft polymers. These coupling agents were found to be much superior reagents than DEPC regarding racemization. The related monomer and dimer model compounds were also prepared by the same method from 3-aminopentane and (?)-, (+)-, and meso-2,4-diaminopentane, respectively. The dimer models were separated and purified by HPLC to give models for isotactic, heterotactic, and syndiotactic polymer models. The enantiomeric purity of the optically active monomer model was determined by 360-MHz NMR spectroscopy using optically active shift reagents.     

Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase

UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.